You are not allowed to use it on trains with compulsory seat reservation, such as TGV trains. Note that reservation is never compulsory, and I think even not possible in TER trains. Regarding the Intercités trains, reservation is compulsory on some of them. This restriction will not bite you as you will not need to travel on them. If you rely on TER and the other operators, you have a very good network at your disposal.

You are not allowed to travel first class.

With "Mobilis" and "Ticket Jeunes" you are not allowed to access the airports Orly and Roissy by train (RER). Moreover the airport busses, Orlybus and Roissybus, cannot be used with these two kinds of tickets.

You have to be sure that your ticket is indeed valid in the zones you want to travel, for the whole journey. If it isn't, with a Navigo pass, you can purchase a complément de parcours (you need to buy it just before your trip at your origin station). Note that a Navigo monthly or yearly pass (but not a weekly pass) is valid for the whole Île-de-France region on week-ends and public holidays. With Mobilis or Ticket Jeunes Week-end, your pass must be valid for the whole journey.